2V6K

Structure of Maleyl Pyruvate Isomerase, a bacterial glutathione-s- transferase in Zeta class, in complex with substrate analogue dicarboxyethyl glutathione


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 

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This is version 1.3 of the entry. See complete history


Literature

Structure of Bacterial Glutathione-S-Transferase Maleyl Pyruvate Isomerase and Implications for Mechanism of Isomerisation.

Marsh, M.Shoemark, D.K.Jacob, A.Robinson, C.Cahill, B.Zhou, N.-Y.Williams, P.A.Hadfield, A.T.

(2008) J Mol Biol 384: 165

  • DOI: 10.1016/j.jmb.2008.09.028
  • Primary Citation of Related Structures:  
    2JL4, 2V6K

  • PubMed Abstract: 
  • Maleyl pyruvate isomerase (MPI) is a bacterial glutathione S-transferase (GST) from the pathway for degradation of naphthalene via gentisate that enables the bacterium Ralstonia to use polyaromatic hydrocarbons as a sole carbon source. Genome sequencing projects have revealed the presence of large numbers of GSTs in bacterial genomes, often located within gene clusters encoding the degradation of different aromatic compounds ...

    Maleyl pyruvate isomerase (MPI) is a bacterial glutathione S-transferase (GST) from the pathway for degradation of naphthalene via gentisate that enables the bacterium Ralstonia to use polyaromatic hydrocarbons as a sole carbon source. Genome sequencing projects have revealed the presence of large numbers of GSTs in bacterial genomes, often located within gene clusters encoding the degradation of different aromatic compounds. This structure is therefore an example of this under-represented class of enzymes. Unlike many glutathione transferases, the reaction catalysed by MPI is an isomerisation of an aromatic ring breakdown product, and glutathione is a true cofactor rather than a substrate in the reaction. We have solved the structure of the enzyme in complex with dicarboxyethyl glutathione, an analogue of a proposed reaction intermediate, at a resolution of 1.3 A. The structure provides direct evidence that the glutathione thiolate attacks the substrate in the C2 position, with the terminal carboxylate buried at the base of the active site cleft. Our structures suggest that the C1-C2 bond remains fixed so when rotation occurs around the C2-C3 bond the atoms from C4 onwards actually move. We identified a conserved arginine that is likely to stabilize the enolate form of the substrate during the isomerisation. Arginines at either side of the active site cleft can interact with the end of the substrate/product and preferentially stabilise the product. MPI has significant sequence similarity to maleylacetoacetate isomerase (MAAI), which performs an analogous reaction in the catabolism of phenylalanine and tyrosine. The proposed mechanism therefore has relevance to the MAAIs. Significantly, whilst the overall sequence identity is 40% only one of the five residues from the Zeta motif in the active site is conserved. We re-examined the roles of the residues in the active site of both enzymes and the Zeta motif itself.


    Related Citations: 
    • A Gene Cluster Encoding Steps in Conversion of Naphthalene to Gentisate in Pseudomonas Sp. Strain U2
      Fuenmayor, S.L., Wild, M., Williams, P.A.
      (1998) J Bacteriol 9: 2522

    Organizational Affiliation

    Department of Biochemistry and Centre for Molecular Recognition, University of Bristol, School of Medical Sciences, University Walk, Bristol BS81TD, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MALEYLPYRUVATE ISOMERASEA, B214Ralstonia sp. U2Mutation(s): 0 
EC: 5.2.1.2 (PDB Primary Data), 5.2.1.4 (UniProt)
UniProt
Find proteins for O86043 (Ralstonia sp)
Explore O86043 
Go to UniProtKB:  O86043
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO86043
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TGG
Query on TGG

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
GAMMA-GLUTAMYL-S-(1,2-DICARBOXYETHYL)CYSTEINYLGLYCINE
C14 H21 N3 O10 S
PWCIUOASSAHGHI-BIIVOSGPSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.659α = 90
b = 60.34β = 93.22
c = 81.68γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-22
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-24
    Changes: Source and taxonomy